Sodium in PDB 1ud2: Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38)

All present enzymatic activity of Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38):
3.2.1.1;

The structure of Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38), PDB code: 1ud2 was solved by T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.44 / 2.13
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	132.143, 132.143, 132.143, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) (pdb code 1ud2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38), PDB code: 1ud2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:13.1 occ:1.00 O A:ASP194 2.2 13.8 1.0 OD1 A:ASP194 2.3 15.5 1.0 OD1 A:ASN104 2.3 15.9 1.0 O A:HIS235 2.4 20.1 1.0 O A:HOH2011 2.5 11.5 1.0 OD1 A:ASN200 2.5 18.0 1.0 C A:ASP194 3.2 15.8 1.0 CG A:ASN200 3.3 18.9 1.0 ND2 A:ASN200 3.3 13.2 1.0 CG A:ASN104 3.4 17.6 1.0 C A:HIS235 3.4 16.9 1.0 CG A:ASP194 3.5 18.4 1.0 CA A:ASP194 3.7 16.5 1.0 CB A:HIS235 3.8 15.8 1.0 ND2 A:ASN104 3.9 16.2 1.0 O A:ASN104 4.2 13.2 1.0 CA A:HIS235 4.2 17.4 1.0 CB A:ASP194 4.2 16.9 1.0 O A:HOH2015 4.3 13.9 1.0 N A:TYR195 4.3 14.0 1.0 N A:ILE236 4.4 15.7 1.0 OD2 A:ASP194 4.4 16.7 1.0 ND2 A:ASN183 4.4 16.8 1.0 CA A:ILE236 4.6 14.9 1.0 CA A:TYR195 4.6 14.5 1.0 CB A:ASN104 4.6 14.7 1.0 CB A:ASN200 4.8 13.6 1.0 O A:ILE201 4.8 15.2 1.0 C A:ASN104 4.9 14.1 1.0 CG1 A:ILE236 4.9 15.8 1.0 CA A:ASN104 4.9 15.5 1.0 O A:TYR193 5.0 16.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:20.2 occ:1.00 O A:GLY300 2.3 18.0 1.0 OD1 A:ASP404 2.4 21.0 1.0 O A:TYR302 2.4 14.4 1.0 O A:HOH2028 2.4 20.3 1.0 O A:TRP403 2.5 19.7 1.0 OD1 A:ASN427 2.7 15.7 1.0 C A:TRP403 3.3 20.4 1.0 ND2 A:ASN427 3.4 10.6 1.0 CG A:ASN427 3.4 15.4 1.0 C A:TYR302 3.5 19.2 1.0 C A:GLY300 3.5 19.1 1.0 CG A:ASP404 3.5 20.1 1.0 CA A:ASP404 3.7 18.4 1.0 N A:ASP404 3.9 18.4 1.0 N A:TYR302 4.1 19.2 1.0 C A:SER301 4.1 19.6 1.0 O A:HOH2071 4.2 18.6 1.0 CB A:ASP404 4.2 19.4 1.0 N A:ASP303 4.3 17.8 1.0 CA A:ASP303 4.3 16.4 1.0 CA A:GLY300 4.3 19.0 1.0 N A:MET304 4.3 14.8 1.0 CB A:TRP403 4.4 18.8 1.0 CA A:TYR302 4.4 18.4 1.0 O A:SER301 4.4 20.1 1.0 CA A:TRP403 4.4 21.5 1.0 N A:SER301 4.4 17.7 1.0 CD1 A:TRP403 4.5 24.3 1.0 OD2 A:ASP404 4.5 20.9 1.0 CA A:SER301 4.5 20.2 1.0 CG A:MET304 4.6 16.0 1.0 C A:ASP303 4.8 16.5 1.0 CG A:TRP403 4.9 24.0 1.0 CB A:ASN427 4.9 11.7 1.0 C A:ASP404 5.0 17.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:14.8 occ:1.00 OD1 A:ASP325 2.2 10.0 1.0 O A:SER337 2.3 16.4 1.0 O A:VAL324 2.3 12.9 1.0 OD1 A:ASN289 2.5 17.2 1.0 CG A:ASP325 2.9 10.9 1.0 C A:SER337 3.4 16.0 1.0 OD2 A:ASP325 3.4 8.9 1.0 C A:VAL324 3.5 10.7 1.0 CG A:ASN289 3.5 17.1 1.0 CG2 A:VAL339 3.6 11.1 1.0 CA A:ASP325 3.8 13.4 1.0 OG1 A:THR329 3.8 11.7 1.0 CB A:ASP325 4.0 10.9 1.0 OG A:SER337 4.0 12.7 1.0 ND2 A:ASN289 4.0 16.2 1.0 CB A:THR329 4.1 11.9 1.0 N A:VAL339 4.1 13.1 1.0 N A:ASP325 4.1 12.4 1.0 CA A:TRP338 4.2 13.5 1.0 N A:TRP338 4.2 15.8 1.0 O A:ASN289 4.3 16.2 1.0 CB A:SER337 4.3 14.4 1.0 CG2 A:THR329 4.4 13.1 1.0 C A:TRP338 4.4 12.9 1.0 CA A:SER337 4.5 15.8 1.0 CB A:VAL339 4.6 12.9 1.0 CA A:VAL324 4.7 11.3 1.0 CB A:ASN289 4.7 13.4 1.0 C A:ASN289 4.9 14.9 1.0 CA A:VAL339 4.9 14.1 1.0 CA A:ASN289 5.0 13.8 1.0 CB A:TYR293 5.0 18.4 1.0

T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki. Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) and Its Sodium Ion Binding Sites J.Biol.Chem. V. 278 24818 2003.
ISSN: ISSN 0021-9258
PubMed: 12719434
DOI: 10.1074/JBC.M212763200